Mutagenetix > Incidental Mutation

Incidental Mutation 'R1769:Pnpt1'

194717

Institutional Source

Beutler Lab

Gene Symbol

Pnpt1

Ensembl Gene

ENSMUSG00000020464

Gene Name

polyribonucleotide nucleotidyltransferase 1

Synonyms

PNPase, polynucleotide phosphorylase, 1200003F12Rik

MMRRC Submission

039800-MU

Accession Numbers

Essential gene?

Essential (E-score: 1.000) question?

Stock #

R1769 (G1)

Quality Score

225

Status

Validated

Chromosome

Chromosomal Location

29130744-29161828 bp(+) (GRCm38)

Type of Mutation

missense

DNA Base Change (assembly)

A to G at 29154159 bp (GRCm38)

Zygosity

Heterozygous

Amino Acid Change

Asparagine to Aspartic acid at position 540 (N540D)

Ref Sequence

ENSEMBL: ENSMUSP00000020756 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000020756]

AlphaFold

Q8K1R3

PDB Structure

Solution structure of the alpha-helical domain from mouse hypothetical PNPase [SOLUTION NMR]

Predicted Effect

probably benign
Transcript: ENSMUST00000020756
AA Change: N540D

PolyPhen 2 Score 0.221 (Sensitivity: 0.91; Specificity: 0.88)

SMART Domains

Protein: ENSMUSP00000020756
Gene: ENSMUSG00000020464
AA Change: N540D

Domain	Start	End	E-Value	Type
low complexity region	4	26	N/A	INTRINSIC
Pfam:RNase_PH	52	183	1.9e-16	PFAM
Pfam:RNase_PH_C	186	251	3.8e-13	PFAM
Pfam:PNPase	282	363	3.7e-9	PFAM
Pfam:RNase_PH	366	501	3.4e-22	PFAM
Pfam:RNase_PH_C	504	581	7.1e-6	PFAM
KH	604	669	8e-7	SMART
S1	677	750	2.15e-4	SMART

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000154924

Meta Mutation Damage Score

0.1198

Coding Region Coverage

1x: 97.5%
3x: 96.9%
10x: 95.3%
20x: 92.5%

Validation Efficiency

100% (91/91)

MGI Phenotype

FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] The protein encoded by this gene belongs to the evolutionary conserved polynucleotide phosphorylase family comprised of phosphate dependent 3'-to-5' exoribonucleases implicated in RNA processing and degradation. This enzyme is predominantly localized in the mitochondrial intermembrane space and is involved in import of RNA to mitochondria. Mutations in this gene have been associated with combined oxidative phosphorylation deficiency-13 and autosomal recessive nonsyndromic deafness-70. Related pseudogenes are found on chromosomes 3 and 7. [provided by RefSeq, Dec 2012]
PHENOTYPE: Mice homozygous for a knock-out allele exhibit embryonic lethality and impaired mitochondrial RNA import. [provided by MGI curators]

Allele List at MGI

Other mutations in this stock

Total: 91 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
4921507P07Rik	A	G	6: 50,591,821		probably benign	Het
A430033K04Rik	A	G	5: 138,646,257	I135V	probably benign	Het
Abca1	T	A	4: 53,074,325	K1119N	probably damaging	Het
Abcb10	C	T	8: 123,962,052	G495D	probably damaging	Het
Abcc9	T	C	6: 142,627,468		probably benign	Het
Akap3	A	G	6: 126,865,846	E476G	possibly damaging	Het
Aldh3b1	A	G	19: 3,918,740	F271S	probably damaging	Het
Alkbh2	C	T	5: 114,124,226	E148K	probably damaging	Het
Ascc3	T	C	10: 50,700,490	V847A	probably damaging	Het
Best3	A	G	10: 117,023,978	N381S	probably benign	Het
Blm	A	T	7: 80,513,370	S78T	probably benign	Het
Bmpr2	T	A	1: 59,868,361	L871Q	probably damaging	Het
Car13	T	A	3: 14,650,735	H104Q	probably benign	Het
Ccdc39	T	C	3: 33,826,480	K446R	probably damaging	Het
Ccnb1ip1	T	C	14: 50,792,111	M165V	probably benign	Het
Cd4	A	T	6: 124,866,655	M431K	possibly damaging	Het
Cdh7	C	T	1: 110,052,876	T178I	probably damaging	Het
Ceacam3	C	T	7: 17,158,376	T348I	probably damaging	Het
Cfap54	C	T	10: 92,904,263		probably null	Het
Clcn6	A	T	4: 148,014,301		probably null	Het
Csf3	A	G	11: 98,702,420	Y121C	probably damaging	Het
Csmd3	C	T	15: 47,704,109		probably benign	Het
Cyp2c69	A	G	19: 39,876,371	I221T	probably benign	Het
Dgcr2	T	C	16: 17,857,251		probably benign	Het
Dhcr7	T	C	7: 143,847,513	F474S	probably damaging	Het
Dnah1	T	C	14: 31,310,882	I399V	probably null	Het
Efcab14	T	A	4: 115,752,991	L183Q	probably damaging	Het
Elmsan1	G	A	12: 84,158,350		probably benign	Het
Evx2	A	G	2: 74,659,157	V88A	probably benign	Het
Exph5	A	G	9: 53,373,809	N730S	probably benign	Het
Farsb	T	A	1: 78,466,983	K196I	probably benign	Het
Fbln7	C	T	2: 128,893,762		probably benign	Het
Fhdc1	A	G	3: 84,448,778	F453S	probably damaging	Het
Gast	T	A	11: 100,336,858	W89R	probably damaging	Het
Gata2	A	G	6: 88,205,255	S402G	probably benign	Het
Gin1	T	A	1: 97,792,437	S386T	probably benign	Het
Golgb1	A	G	16: 36,916,001	E1870G	probably damaging	Het
Hivep3	T	A	4: 120,097,571	V1028E	possibly damaging	Het
Ifi203	G	A	1: 173,928,760	R486*	probably null	Het
Ifi209	G	A	1: 173,641,162	S186N	probably benign	Het
Ifih1	C	T	2: 62,606,394	A562T	probably damaging	Het
Itch	T	C	2: 155,172,561	L106S	probably damaging	Het
Itga4	T	A	2: 79,315,706		probably null	Het
Kdm4c	A	G	4: 74,280,997	S141G	possibly damaging	Het
Kirrel	C	T	3: 87,089,151	M380I	probably null	Het
Klra3	T	C	6: 130,330,263		probably null	Het
Lama2	A	T	10: 27,208,406	S923T	probably damaging	Het
Lama2	G	C	10: 27,208,407	F922L	probably benign	Het
Llgl1	G	A	11: 60,707,047	V331M	probably damaging	Het
Lrrc30	T	C	17: 67,631,681	*301W	probably null	Het
Map1lc3b	C	T	8: 121,593,487		probably benign	Het
Mbd2	A	G	18: 70,616,619	I302V	probably benign	Het
Med27	A	G	2: 29,500,295	Y78C	probably damaging	Het
Mei1	C	T	15: 82,112,570		probably null	Het
Miga1	T	C	3: 152,287,554	E346G	probably damaging	Het
Myef2	A	G	2: 125,115,443	S131P	probably damaging	Het
Myocd	T	C	11: 65,178,701	H899R	probably benign	Het
Ncam1	A	G	9: 49,545,256		probably benign	Het
Ngf	T	A	3: 102,520,197	N87K	possibly damaging	Het
Nol10	T	A	12: 17,416,708		probably benign	Het
Nrip2	A	G	6: 128,408,268	I221V	probably benign	Het
Nup205	G	A	6: 35,205,431	G777D	probably damaging	Het
Olfr1446	A	G	19: 12,889,683	V298A	probably damaging	Het
Olfr199	A	G	16: 59,215,981	F211L	probably benign	Het
Olfr802	T	A	10: 129,682,212	T176S	probably benign	Het
Olfr855	A	T	9: 19,585,386	Q283L	probably damaging	Het
Olfr974	G	T	9: 39,942,955	D232Y	probably benign	Het
Oxt	A	T	2: 130,576,300	R31W	probably damaging	Het
Pde4dip	A	G	3: 97,695,930	S2248P	probably benign	Het
Pias1	A	G	9: 62,952,178	V16A	probably damaging	Het
Pkp2	T	C	16: 16,262,697	S616P	probably damaging	Het
Plch2	T	C	4: 155,000,083	Y379C	probably damaging	Het
Ptpn23	G	A	9: 110,391,678	H255Y	possibly damaging	Het
Rad21	T	C	15: 51,972,307	N237D	probably benign	Het
Ryr3	A	C	2: 112,751,768		probably null	Het
Sgk1	C	A	10: 21,997,108		probably benign	Het
Slc1a5	G	T	7: 16,797,539	A490S	probably damaging	Het
Slc5a8	T	C	10: 88,919,464	Y478H	probably benign	Het
Slc5a8	T	A	10: 88,919,466	Y478*	probably null	Het
Slc9a3	A	T	13: 74,163,071	M562L	probably benign	Het
Thsd7a	G	A	6: 12,555,715	R57*	probably null	Het
Tiam1	T	C	16: 89,860,279	R690G	probably damaging	Het
Tmem150b	A	G	7: 4,724,366	S47P	probably damaging	Het
Trim39	C	T	17: 36,263,940	R190Q	probably damaging	Het
Ttc32	A	T	12: 9,035,073	I98L	possibly damaging	Het
Vps13c	A	G	9: 67,965,721	T3304A	probably benign	Het
Wdr35	A	C	12: 9,012,728	D638A	probably damaging	Het
Wwc1	G	T	11: 35,861,844	P797T	probably benign	Het
Zan	T	A	5: 137,464,518	T800S	unknown	Het
Zbbx	A	G	3: 75,083,619		probably benign	Het
Zufsp	T	C	10: 33,935,176	M291V	probably damaging	Het

Other mutations in Pnpt1

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
IGL00229:Pnpt1	APN	11	29154217	critical splice donor site	probably null
IGL00920:Pnpt1	APN	11	29157087	splice site	probably benign
IGL01358:Pnpt1	APN	11	29138425	missense	possibly damaging	0.95
IGL01454:Pnpt1	APN	11	29137142	missense	probably benign	0.19
IGL01622:Pnpt1	APN	11	29148272	splice site	probably benign
IGL01623:Pnpt1	APN	11	29148272	splice site	probably benign
IGL01674:Pnpt1	APN	11	29155787	missense	probably benign	0.00
IGL01802:Pnpt1	APN	11	29154306	missense	probably damaging	1.00
IGL02222:Pnpt1	APN	11	29159327	missense	possibly damaging	0.71
IGL02222:Pnpt1	APN	11	29130842	missense	probably benign	0.00
IGL02616:Pnpt1	APN	11	29135505	splice site	probably benign
IGL02859:Pnpt1	APN	11	29138162	missense	probably damaging	1.00
IGL02965:Pnpt1	APN	11	29156939	missense	probably damaging	0.98
IGL03121:Pnpt1	APN	11	29132845	missense	probably benign	0.03
PIT4651001:Pnpt1	UTSW	11	29156945	critical splice donor site	probably null
R1023:Pnpt1	UTSW	11	29141328	splice site	probably benign
R1477:Pnpt1	UTSW	11	29137102	missense	probably benign	0.14
R1524:Pnpt1	UTSW	11	29130776	missense	unknown
R1839:Pnpt1	UTSW	11	29154342	missense	possibly damaging	0.82
R1975:Pnpt1	UTSW	11	29141256	missense	probably benign	0.16
R1977:Pnpt1	UTSW	11	29141256	missense	probably benign	0.16
R1996:Pnpt1	UTSW	11	29141679	missense	probably benign	0.01
R3771:Pnpt1	UTSW	11	29138174	missense	probably benign	0.05
R4346:Pnpt1	UTSW	11	29145478	missense	probably damaging	1.00
R4423:Pnpt1	UTSW	11	29153375	splice site	probably null
R5354:Pnpt1	UTSW	11	29154166	missense	probably damaging	1.00
R5503:Pnpt1	UTSW	11	29138156	missense	probably damaging	1.00
R5514:Pnpt1	UTSW	11	29153246	missense	possibly damaging	0.82
R5908:Pnpt1	UTSW	11	29130887	missense	probably benign	0.00
R6225:Pnpt1	UTSW	11	29145469	missense	probably benign	0.38
R6605:Pnpt1	UTSW	11	29138567	missense	possibly damaging	0.69
R7096:Pnpt1	UTSW	11	29154867	missense	probably benign	0.03
R7214:Pnpt1	UTSW	11	29137285	missense	probably damaging	1.00
R7365:Pnpt1	UTSW	11	29161334	missense	probably damaging	1.00
R7492:Pnpt1	UTSW	11	29135522	missense	probably benign	0.01
R7497:Pnpt1	UTSW	11	29130860	missense	probably benign	0.00
R7686:Pnpt1	UTSW	11	29157070	missense	probably damaging	0.97
R8166:Pnpt1	UTSW	11	29156875	missense	probably benign
R8309:Pnpt1	UTSW	11	29153277	missense	probably benign	0.01
R8389:Pnpt1	UTSW	11	29130758	start codon destroyed	unknown
R8542:Pnpt1	UTSW	11	29132773	splice site	probably null
R8737:Pnpt1	UTSW	11	29154815	critical splice acceptor site	probably null
R8876:Pnpt1	UTSW	11	29146769	intron	probably benign
R9308:Pnpt1	UTSW	11	29147535	critical splice donor site	probably null
R9545:Pnpt1	UTSW	11	29156840	missense	probably benign	0.13
Z1176:Pnpt1	UTSW	11	29145475	missense	probably benign	0.00
Z1176:Pnpt1	UTSW	11	29145477	missense	possibly damaging	0.80

Predicted Primers

PCR Primer
(F):5'- CGATTGAACAGCAATCAAGCAGCAG -3'
(R):5'- GGAACAAGGCACACTGACTTACCTG -3'

Sequencing Primer
(F):5'- CAGAGGTGGCTCTTTGCATTTAAC -3'
(R):5'- ACACTGACTTACCTGACGCTTG -3'

Posted On

2014-05-23